But there’s an obvious problem with this. That stuff we’re turning into fuel is also food for humans and feed for animals.

(And as an aside, how come we always call it “animal feed” as opposed to “animal food”? And why don’t we ever refer to “human feed”? Hmm?)

A lot of the plant is wasted when you grow crops for fuel or food. The leaves and stems, with their tough cell walls made of cellulose, hemicellulose and lignin, are more of a nuisance than anything else. Wouldn’t it be great if there were a use for what is now plowed under or burned?

There is, or there soon will be, thanks to research aimed at using bacteria to convert this “lignocellulosic biomass” into fuel in its own right.

A just-published article in Nature reveals the state of the art. Titled “Microbial production of fatty-acid-derived fuels and chemicals from plant biomass,” it describes the successful engineering of the common bacterium Excherichia coli–better known as E. coli and generally in the news when it contaminates water or meat and makes people sick–into a producer of biodiesel.

One of the co-authors of the research study is Jay Keasling, chief executive officer for the U.S. Department of Energy’s Joint BioEnergy Institute (JBEI). “We’ve got a billion tons of biomass every year that goes unused,” he says, adding that fuel produced from that biomass could make up for as much as half of U.S. oil imports, turning “the U.S. Midwest into the new ‘Mideast’.”

That’s not hyperbole: by one estimate, lignicellulosic biomass could produce more than 7,500 litres of renewable petroleum per acre.

The researchers modified the E. coli genome, inserting genetic code for the production of an enzyme called hemicellulase, which can break down hemicellulose into smaller sugar molecules which E. coli can then turn into fatty acids.

E. coli normally produces only as much of the fatty acids as it needs for its own cell membranes. But the researchers’ E. coli were further modified so that the fatty acids just kept coming, turning each bacterium into a microscopic biodiesel factory.

The process takes place in fermentation vats, into which the bacteria expel little drops of oil. Turn off the impellers, and the oil floats to the top, where it can be skimmed off.

Even better, by tweaking the process, chemical products ranging from solvents to lubricants to jet fuel could conceivably be produced.

Of course, it’s important to note that the research reported in Nature is just a proof of concept. There’s no commercially viable process for doing any of this yet–but Keasling hopes there will be within a very few years. Work will continue as the researchers search for ways to make use of even more of what’s in the feedstock–not just the hemicellulose.

There’s already a company standing ready to market fuels and other microbe-produced chemicals. Based in California, LS9, founded by a geneticist and a plant biologist, helped fund the research reported in Nature. LS9 points out that the crude oil produced by bioengineered bacteria has none of the contaminating sulfur of regular crude oil, so it’s cleaner. And despite its unorthodox origins, it can be refined like any other crude oil in a standard refinery.

There are other companies pursuing their own paths. Amyris Biotechnologies, for example, says it has also created bacteria capable of providing renewable hydrocarbon-based fuels. There are many more.

Why would this be preferable to ethanol production as it is currently carried out? Aside from the aforementioned fact that we’re presently turning food into fuel, hydrocarbon fuels are more efficient than ethanol, packing about 30 percent more energy into any given quantity. And even better, they take less energy to produce: ethanol production, which involves distilling, requires 65 percent more energy than hydrocarbon production does.

Perhaps the oil industry will slowly evolve away from the purview of drilling companies and into the realm of agriculture.

As for the marketing slogan for this new germ-produced form of fuel, I think I’ve come up with a winner: “E. coli. It’s not just for food poisoning anymore.”

What do you think?

Fermenting the sugars found in corn or other grains into ethanol has been around for a long time, of course, and it’s pretty much a proven technology. On the other hand, do we really want to be turning food into fuel?

More promising have been recent advances in turning lignocellulose, the stuff that makes up the cell walls in plants, into ethanol and other fuels: that would allow us to use grasses, wood chips, straw and other non-food as biomass.

Now comes word of a fuel-producing technology that doesn’t require biomass of any sort: just carbon dioxide and sunlight. And no, I’m not talking about trees.

On Monday, a Massachussetts company called Joule Biotechnologies announced that it has the technology to convert carbon dioxide directly into transportation fuels and chemicals. Not only that, they say, “this eco-friendly, direct-to-fuel conversion requires no agricultural land or fresh water.”

The company was founded in 2007, and relies on something it calls “Helioculture” technology, mixing, as the New York Times’s article on the announcement puts it, “CO2, Slime and Sunshine.”

More specifically, the company grows genetically engineered microorganisms in specially designed bioreactors. The microorganisms are photosynthetic, able to use energy from the sun to convert carbon dioxide and water into ethanol or hydrocarbon fuels.

The process works well in the laboratory, so the real question is if it can be scaled up to an industrial-sized plant. To find out, Joule plans to break ground on a modular pilot plant early in 2010 that will produce ethanol (trademarked as SolarEthanol), and the following year hopes to begin construction on a commercial-scale operation that can also produce hydrocarbons and associated chemicals, “several of which have already been demonstrated at laboratory scale.

It’s looking for sites near CO2 producers such as coal-fired power plants and cement kilns, with locations in Texas, Arizona, Nevada and New Mexico, places with lots of sun and lots of space, under consideration

Open spaces are needed because a large plant would look a lot like a solar array: a huge field covered with panels, except these panels, rather than producing electricity, would produce liquid fuels

The company estimates that a single acre covered with its “SolarConverter” panels (flat, transparent, and about the size of a sheet of plywood) could produce 20,000 gallons of ethanol at a cost of $50 a barrel. (That makes it competitive with oil, although it’s worth noting that that price includes existing subsidies: what the unsubsidized cost would be, I don’t know.)

At that level of production, if you built enough plants to cover, in total, an area the size of the Texas panhandle, you could meet all of the United States’ transportation fuel needs.

In Technology Review, writer Kevin Bullis notes that the company’s technology sounds similar to that of biofuels produced by algae—but the company says it is not using algae, and its stated production estimates are an order of magnitude greater than algae-based biofuels, which are estimated to have potential yields of only 2,000 to 6,000 gallons per acre.

Its estimated cost of production is also only a fraction of that of algae-based biofuels, which currently would require crude oil to rise to $800 a barrel in order to be competitive.

Besides, algae produces oils that have to be refined, whereas Joule says its microorganisms will produce ethanol or hydrocarbons directly. The Joule microorganisms also excrete the fuels, whereas algae has to be harvested and processed to extract oil.

Too good to be true? Maybe. But there are other companies in the race to develop the same kinds of technology. And with the push to reduce carbon dioxide emissions and move away from fossil fuels, that race is only going to get hotter.

So remember the name: Joule Biotechnologies.

Someday, its genetically modified critters could be cheerfully churning out the fuel that powers your car.

I’m a sensitive kinda guy. I fact, I’m so sensitive I sometimes tear up just during the process of making dinner.

It’s not that I’m overcome with emotion at the blessing of having at my disposal the wherewithal to stir-fry. (I’m not that sensitive.) No, it’s usually because I’m slicing onions.

Onions have been a part of the human diet since prehistoric times. We don’t even know where they originated: some say central Asia, others Iran or West Pakistan. (So I learned from the interesting history of onions I found on the website of the U.S.’s National Onion Association, an organization whose very existence had heretofore escaped me.)

Once humans started farming, onions may have been one of their very first crops. They’re less perishable than many, can be easily transported, and will grow in a variety of soils and climates. They’re full of water, so they help prevent thirst, but they can also be dried and stored for eating later when food is scarce.

Chinese gardens had onions 5,000 years ago. The Egyptians, for whom the onion symbolized eternity, buried them with their Pharaohs and frequently depicted them in religious imagery. Onions are mentioned in the Bible The ancient Greeks fed onions to athletes to fortify them for the Olympic Games.

Onions were a staple in the Middle Ages in Europe, and the first Europeans brought onions with them to North America—only to discover the First Nations people were already using onions in a variety of ways.

But for all those thousands of years, onions made people cry once they were sliced open. The reason: when you break open the cells of an onion, you release enzymes that decompose some of the other substances that escape from the broken cells, forming sulfenic acids which escape the onion as a volatile gas.

This gas reacts with the water on your eyes to form, among other things, a mild sulfuric acid—very irritating, as you’d expect. When your eyes are irritated, they produce extra tears in an attempt to dilute or wash away the irritating substance. (A process we contact-lens wearers are particularly familiar with.)

But your teary-eyed onion-cutting days may soon be over, for recently in The Netherlands, at the Fifth International Symposium on Edible Alliaceae (Super Bowl, Schmuper Bowl—what an event that must have been!) Dr. Colin Eady of The New Zealand Institute for Crop & Food Research (one of their Crown corporations) announced that he and his Japanese collaborators have been successfully produced and tested tearless onions in the laboratory.

How do you take the tears out of an onion? By silencing the lachrymatory factor synthase gene, which tells the onion’s cells to turn sulfur compounds into the chemical that decomposes into the sulfenic acids that causes your eyes to sting. With that gene silenced, the sulfur compounds that would normally go into that chemical are instead available for the onion to turn into other compounds that contribute to the flavor and health benefits the onion provides.

Better yet, the gene silencing technology does not involve genetic engineering as it is usually thought of: no genes are introduced from other species, so no proteins show up in the onions that aren’t already present in onions. It’s a process of subtraction, rather than addition.

The announcement hit the onion world like a bombshell. Dr. Eady’s work was featured on the front cover of Onion World magazine’s final issue of 2007. The magazine quoted renowned onion scientist Dr. Michael J. Havey, a professor of horticulture at the University of Wisconsin, as saying that Dr. Eady’s work was the number one topic of discussion at the symposium in The Netherlands. Dr. Havey predicts that tearless onions will eventually become a mainstay in kitchens around the world.

When you cut an onion and your eyes well up, you are part of a great unbroken link of weepy-eyed onion-cutters dating back through millennia to before the dawn of civilization. It’s astonishing to think that, if this research pans out, that link may soon be severed.

But you know what? Sensitive though I am, I won’t shed a tear over it.

Efforts to genetically modify large animals have been hindered by the fact that the two methods currently used to effect it, somatic cell nuclear transfer or pronuclear injection, are costly, inefficient, difficult, and carry a risk of producing abnormal offspring. Now researchers at the University of Pennsylvania School of Veterinary Medicine have successfully produced genetically modified mice and goats by transferring modified genetic information via a harmless virus to male reproductive cells, which then passed the modification on naturally to about 10 percent of the offspring. In other words, genetic modification via gene therapy.

Of course, using this technique on humans in combination with in-vitro fertilization and careful weeding of the resulting embryos in order to create a genetically modified super race with abilities surpassing normal humans’ would be completely illegal and unethical, and only a deranged science fiction writer such as myself whose next book features genetically modified humans would even think of it as a possibility.

So, no worries.

(Via PhysOrg.)

(Also posted to Futurismic.)

Since the column was written the company has been a bit down on its luck, as this year-old story from the National Post makes clear:

Nexia Biotechnologies Inc. was a small firm with a neat idea: making spider silk by splicing genes from arachnids into goats and harvesting the silk protein, or “BioSteel” from their milk. BioSteel was demonstrated to be stronger and lighter than steel or Kevlar.

Between 1993 and 2000, Nexia raised $67-million and went public. But by last year, the Montreal-based firm had spent most of its cash and sold part its business for shares in another speculative biotech outfit.

It was left with a herd of 40 “franken-goats,” some patents and $2.2-million in cash. “BioSteel remains an interesting research project, but the dilemma remains what is the end use of the product?” says founder Jeffrey Turner.

However, things may be looking up. In October came this news:

Enseco Energy Services Corp. (“Enseco”) and Nexia Biotechnologies Ltd. (formerly, 6539718 Canada Inc.) (“New Nexia”) are pleased to announce the successful completion of the previously announced arrangement involving Nexia Biotechnologies Inc. (“Nexia”), Enseco Energy Services Corp. (“Private Enseco”), New Nexia and Enseco Management Corp. (“ManagementCo”).

The Arrangement resulted in the amalgamation of Nexia, Private Enseco and ManagementCo to form “Enseco Energy Services Corp”, a new oil and gas service industry company and the creation of New Nexia which will continue to pursue Nexia’s biotechnology opportunities.

And now, according to the most recent Nexia press release, which announces the company is now trading on Canada’s newest stock exchange, the CNQ:

Nexia has received an Issue Notification from the United States Patent and Trademark Office, for U.S. Patent No. 7,157,615. This patent strengthens and protects our intellectual property with respect to the production of biofilaments in transgenic animals.

Nexia has shipped transgenic goat milk to the University of Wyoming where BioSteel® is being purified and made available for research in industrial, medical device and nanotech applications. Nexia welcomes back Dr. Costas Karatzas, the former Senior VP of R&D of Nexia Biotechnologies Inc., as a consultant, who will assist in pursuing all possible strategies to maximize shareholder value.

So the work continues. My question is, why all the visitors today? Was there some big news story about spider silk proteins produced from goat’s milk that I missed?

Anyone?

Installing one of those prefab, snap-together wood-flooring kits is a lot easier than shaping and sanding rough planks. Adapting a similar construction strategy, a biotech startup called Codon Devices, based in Cambridge, MA, aims to streamline genetic engineering. It makes made-to-order DNA strands, freeing scientists from the finicky work it takes to put together a complicated piece of DNA the old-fashioned way.

That capability could soon change the face of molecular biology. As it becomes cheaper and cheaper to create large chunks of genetic material from scratch, scientists will be able to make ever more complex biological creations. “In the next few years, we’ll probably see people engineering cells to do drug delivery or creating cellular sensors,” says George Church, a professor of genetics at Harvard and one of Codon’s founders. “Maybe even cells that make inorganic objects of interest, like nanostructures.”

(Via KurzweilAI.net.)

“The exciting finding is that we have been able to reduce gossypol – which is a very toxic compound – from cottonseed to a level that is considered safe for consumption,” said Dr. Keerti Rathore, Texas Agricultural Experiment Station plant biotechnologist. “In terms of human nutrition, it has a lot of potential.” The cottonseed from these plants meet World Health Organization and U.S. Food and Drug Administration standards for food consumption, he said, potentially making the seed a new, high-protein food available to 500 million people a year.

Around 40 million Christmas trees are harvested every year in the U.S. and Canada, most from Christmas tree farms. A small to medium tree farm will harvest 10,000 trees, and some of the multinational giants harvest up to a million trees annually on plantations from North Carolina to Nova Scotia.

(Christmas tree farms, by the way, are also oxygen farms. One acre of Christmas trees produces the daily oxygen requirement for 18 people. Since there are a million acres of Christmas trees being grown at any given time, every day Christmas trees produce enough oxygen for18 million people!)

Only one in every 10,000 Christmas trees is perfect. Most develop gaps or unsightly branches, so growers prune their trees every June from the age of three on, and cut off the bottom branches to give the trees “handles” long enough for tree stands.

That kind of labor may soon be a thing of the past, however. Many different research teams are attempting to clone perfect trees, instead of relying on Nature to produce them. For instance, a group at Michigan State University is working on cloning Douglas fir and Scotch pine. First, they search the Christmas tree farm for a specimen with a straight trunk (so it slips easily into the stand), the strength to hold lots of ornaments, thick needles and good needle retention, good color, branches that angle up at 45 degrees and a uniform conical shape. Right now, cloned trees are expensive, but once they can be mass-produced, the price should come down.

The next step is to genetically modify the trees to resist the fungal diseases and soil-dwelling insect larvae that plague them. A farm growing disease-and-insect-resistant clones could sell 95 percent of its crop, compared to just 60 to 70 percent today, and greatly reduce the use of pesticide. Trees could also be modified to keep their needles longer and grow faster, decreasing the time from planting to harvesting.

Evergreens have proven difficult to genetically engineer, but a Danish team led by Dr. Jens Find, working with the New Zealand Institute of Forest Research, is even now nursing 1,500 cloned and genetically engineered fir seedlings. If this test is successful, cloned and genetically engineered Christmas trees could be on sale within five years. (Dr. Find says he’s had no negative reaction from the forces fighting genetically modified foods: “After all, it’s not as if anyone ate Christmas trees.”)

As long as you’re engineering a better Christmas tree, why stop with disease and insect resistance? Five postgraduate students at the University of Hertfordshire, UK, don’t see any reason to. As their entry in a competition where students have to develop plans for a fictitious start-up biotechnology company, they proposed developing and marketing a self-illuminating Christmas tree.

Genetic engineers have already creating glowing mice, silk and potatoes, so the idea isn’t far-fetched. The tree, a Douglas spruce, would glow green in the dark and produce a noticeable light even during the day. It would have two genes from fluorescent jellyfish and fireflies added to it. The first produces a substance called green fluorescent protein (GFP), while the second produces an enzyme called luciferase.

The trees would be infected with a harmless bacterium carrying the two genes. That alone wouldn’t make the tree glow; to activate the luciferase and make the GFP glow, you’d first have to fertilize the tree with a chemical compound called luciferin, sold along with the tree.

Although the genes for green fluorescence are the most widely used by genetic engineers (they make it easy to tell if they’ve successfully introduced a gene into an organism), blue fluorescent proteins are also known, and recently a red fluorescent protein was found in a coral. Which means, in theory, you could create a Christmas tree that would grow its own multicolored lights.

Aat this point, nobody is actually trying to make such a tree. On the other hand, the students’ entry has advanced to the finals of the competition, so who knows? Maybe they’ll make their fictitious company a reality.

The students estimate that the initial trees would cost around £200. Nevertheless, said one, “I’m sure a lot of people would love them, especially the Americans.”

Cloned, genetically altered goats producing spider silk in their milk sounds like something out of The X-Files, but it was in all the papers last week when a company called Nexia revealed it had cloned three goats (Clint, Danny and Arnold), and explained why.

The cloning of goats brings to four (sheep, mice, cows and goats) the number of species that have been cloned since Dolly the sheep made headlines a couple of years ago, using a process called nuclear transfer.

A clone is an exact genetic copy of an existing animal. Every cell in an animal’s body contains the complete genetic information for the entire animal within its nucleus. In nuclear transfer cloning, cells are taken from the animal to be cloned, then the DNA is removed from the nuclei. The DNA is transferred into mature, unfertilized eggs, which begin developing, just as if they’d been fertilized. The embryos are then transferred into surrogate mothers.

Each of the Montreal goats is essentially an identical twin of the original goat. They all have the same markings and the same head and body shapes.

Nexia didn’t clone Clint, Danny and Arnold because of a shortage of goats. Nexia wants to create an entirely different breed of goats: goats that have been genetically altered to produce a substance similar to spider silk in their milk.

If you’ve just decided to swear off goat cheese, relax: the milk wouldn’t be for human consumption. The goal is to retrieve the spider-silk proteins from the milk and turn them into a substance called BioSteel, an incredibly light fabric both biodegradable and strong enough to stop bullets. Nexia thinks BioSteel could be used in everything from body armor to spacecraft construction. It could replace plastics and other materials the body typically rejects for artificial tendons, ligaments and other prostheses. It could make super-thin, biodegradable sutures for eye or brain surgery. It could even strengthen the structural steel used in buildings. (Although it would have to be carefully sealed from the environment so bacteria wouldn’t eat it.)

Spider silk is made of a protein whose molecules are capable of making lots of bonds with neighboring molecules. As spiders secrete this protein, it hardens and pulls taut, crystallizing into a strong cable able to withstand the impact of a hurtling fly.

There’s a strong similarity between the way mammals make milk proteins and spiders make silk proteins. Nexia believes they can introduce the gene from spiders that causes certain cells to produce silk into goats, tricking the goats’ mammary glands into producing silk along with milk. The goats would become biological factories.

Once Nexia has goats containing the spider-silk gene, it will clone them, then breed them normally to produce a herd of goats, all of which contain the spider-silk gene.

Nexia at first indicated they had been the first to clone goats, but it turns out three goats were cloned in the U.S. last fall, for a similar reason: they’ve been genetically modified to produce an anti-blood clotting protein, called Antithrombin III, in their milk. Antithrombin III is currently undergoing human tests.

These advances have many people concerned. Every advance in cloning makes it more likely that someone will try to clone a human, which critics feel threatens the integrity of being human. “Every human has a right to have their life as a surprise. We have a right not to be manufactured,” is how Dr. Margaret Somerville, an ethicist at McGill University, puts it.

Others see a nightmare world in which clones are created simply to provide body parts. Since the clones would be genetically identical, organs from them would not be rejected by the original’s body.

Many people are pushing for laws banning human cloning, and the federal government announced the day after the Montreal scientists announced the birth of Danny, Clint and Arnold that it will soon introduce such legislation.

The cloning of animals isn’t as big an ethical concern in most people’s minds, since we already use animals to provide food and clothing. But there are concerns about the cross-species exchange of genes. Critics point out that living systems are so much more complicated than we appreciate that we can’t know what consequences cross-species engineering will have.

But the beneficial possibilities of herds of dairy animals able to produce drugs and other valuable substances along with their milk are so great it’s such research will slow. Just like the old science fiction movies they evoke, the Spider-Goat Clones of Montreal will almost certainly spawn sequels.